Here we provide information about functions or classes that have been removed, renamed or are deprecated (not recommended) during different release circles.
Stats
Welcome to the new module dipy.viz.stats. This module will be used to integrate various analysis.
Tracking
Notes
IO
load_tck and save_tck from dipy.io.streamline has been added. They are highly recommended for managing streamlines.
Gradient Table
The default value of b0_thresold has been changed(from 0 to 50). This change can impact your algorithm.
If you want to assure that your code runs in exactly the same manner as before, please initialize your gradient table with the keyword argument b0_threshold set to 0.
Visualization
dipy.viz.fvtk module has been removed. Use dipy.viz.* instead. This implies the following important changes:
- Use from dipy.viz import window, actor instead of from dipy.viz import fvtk`.
- Use ``window.Renderer() instead of fvtk.ren().
- All available actors are in dipy.viz.actor instead of dipy.fvtk.actor.
- UI elements are available in dipy.viz.ui.
dipy.viz depends on FURY package. To get more informations about FURY, go to https://fury.gl
Streamlines
dipy.io.trackvis module is deprecated. Use dipy.io.streamline instead. Furthermore,
load_trk and save_trk from dipy.io.streamline is highly recommended for managing streamlines.
When you create streamlines, you should use from dipy.tracking.streamlines import Streamlines. This new
object uses much less memory and it is easier to process.
Visualization
dipy.viz.fvtk module is deprecated. Use dipy.viz.* instead. This implies the following important changes:
- Use from dipy.viz import window, actor instead of from dipy.viz import fvtk`.
- Use ``window.Renderer() instead of fvtk.ren().
- All available actors are in dipy.viz.actor instead of dipy.fvtk.actor.
- UI elements are available in dipy.viz.ui.
No major API changes.
Notes
dipy.io.trackvis module will be deprecated on release 0.14. Use dipy.io.streamline instead.
dipy.viz.fvtk module will be deprecated on release 0.14. Use dipy.viz.ui instead.
Dropped support for Python 2.6*
It has been 6 years since the release of Python 2.7, and multiple other versions have been released since. As far as we know, DIPY still works well on Python 2.6, but we no longer test on this version, and we recommend that users upgrade to Python 2.7 or newer to use DIPY.
Tracking
probabilistic_direction_getter.ProbabilisticDirectionGetter input parameters
have changed. Now the optional parameter pmf_threshold=0.1 (previously fixed
to 0.0) removes directions with probability lower than pmf_threshold from
the probability mass function (pmf) when selecting the tracking direction.
DKI
Default of DKI model fitting was changed from “OLS” to “WLS”.
The default max_kurtosis of the functions axial_kurtosis, mean_kurtosis, radial_kurotis was changed from 3 to 10.
Visualization
Prefer using the UI elements in dipy.viz.ui rather than
dipy.viz.widgets.
IO
Use the module nibabel.streamlines for saving trk files and not
nibabel.trackvis. Requires upgrading to nibabel 2+.
** New visualization module**
fvtk.slicer input parameters have changed. Now the slicer function is
more powerfull and supports RGB images too. See tutorial viz_slice.py for
more information.
Interpolation The default behavior of the function core.sphere.interp_rbf has changed. The default smoothing parameter is now set to 0.1 (previously 0). In addition, the default norm is now angle (was previously euclidean_norm). Note that the use of euclidean_norm is discouraged, and this norm will be deprecated in the 0.11 release cycle.
Registration
The following utilty functions from vector_fields module were renamed:
warp_2d_affine is now transform_2d_affine
warp_2d_affine_nn is now transform_2d_affine_nn
warp_3d_affine is now transform_3d_affine
warp_3d_affine_nn is now transform_3d_affine_nn
GQI integration length
Calculation of integration length in GQI2 now matches the calculation in the ‘standard’ method. Using values of 1-1.3 for either is recommended (see docs and references therein).
Peaks
The module peaks is now available from dipy.direction and it can still
be accessed from dipy.reconst but it will be completelly removed in version
0.10.
Resample
The function resample from dipy.align.aniso2iso is deprecated. Please,
use instead reslice from dipy.align.reslice. The module aniso2iso
will be completely removed in version 0.10.
Peaks_from_model
The function peaks_from_model is now available from dipy.reconst.peaks
. Please replace all imports like:
from dipy.reconst.odf import peaks_from_model
with:
from dipy.reconst.peaks import peaks_from_model
Target
The function target from dipy.tracking.utils now takes an affine
transform instead of a voxel sizes array. Please update all code using
target in a way similar to this:
img = nib.load(anat)
voxel_dim = img.header['pixdim'][1:4]
streamlines = utils.target(streamlines, img.get_data(), voxel_dim)
to something similar to:
img = nib.load(anat)
streamlines = utils.target(streamlines, img.get_data(), img.affine)